# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 19:37:16 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C1=C(C)NC(=C(C1c2ccccc2[N](=O)=O)C(=O)OC)C
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 C5U  C5U  'dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate'  ligand  43  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C5U
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 C5U  C10  C  C      0   0.577   2.5907   0.4297  -0.7272
 C5U  C13  C  CH3    0  -0.420   3.5066  -1.3863  -1.9186
 C5U  C15  C  CR6    0   0.232   0.0503  -0.8641   0.7792
 C5U  C17  C  CR16   0  -0.216  -0.1250  -1.3101   3.1699
 C5U  C20  C  CR6    0   0.157   0.3148  -2.2246   0.6133
 C5U  C24  C  CH3    0  -0.727   2.5592   3.1005   0.6316
 C5U  O01  O  O      0  -0.456  -2.4913  -0.6822  -0.8975
 C5U  C02  C  C      0   0.577  -2.4057   0.4942  -0.6213
 C5U  O03  O  O2     0  -0.465  -3.4417   1.3238  -0.7085
 C5U  C04  C  CH3    0  -0.420  -4.6949   0.7687  -1.0968
 C5U  C05  C  C      0  -0.168  -1.1535   1.1132  -0.1827
 C5U  C06  C  C      0   0.355  -1.0568   2.3460   0.3713
 C5U  N07  N  NH1    0  -0.714   0.1811   2.8185   0.7186
 C5U  C08  C  C      0   0.367   1.3641   2.2403   0.3561
 C5U  C09  C  C      0  -0.156   1.3502   1.0098  -0.2167
 C5U  O11  O  O      0  -0.467   3.6982   0.9203  -0.6592
 C5U  O12  O  O2     0  -0.476   2.3818  -0.7468  -1.3221
 C5U  C14  C  CH1    0  -0.413   0.0600   0.2101  -0.3092
 C5U  C16  C  CR16   0  -0.311  -0.1535  -0.4413   2.0934
 C5U  C18  C  CR16   0  -0.276   0.1324  -2.6582   2.9669
 C5U  C19  C  CR16   0  -0.261   0.3683  -3.1122   1.6843
 C5U  O22  O  O     -1  -0.359  -0.1412  -2.5115  -1.6254
 C5U  O23  O  O      0  -0.383   1.4192  -3.6741  -0.7552
 C5U  C25  C  CH3    0  -0.735  -2.1634   3.3102   0.6806
 C5U  H1   H  HCH3   0   0.246   3.1262  -2.2880  -2.3888
 C5U  H2   H  HCH3   0   0.237   3.9680  -0.7545  -2.6772
 C5U  H3   H  HCH3   0   0.235   4.2554  -1.6559  -1.1739
 C5U  H4   H  HCR6   0   0.271  -0.3030  -0.9323   4.1679
 C5U  H5   H  HCH3   0   0.250   2.2624   3.9982   1.1721
 C5U  H6   H  HCH3   0   0.268   3.3022   2.5771   1.2275
 C5U  H7   H  HCH3   0   0.270   3.0425   3.4107  -0.2932
 C5U  H8   H  HCH3   0   0.248  -5.4032   1.5918  -1.0760
 C5U  H9   H  HCH3   0   0.235  -4.6543   0.3541  -2.1039
 C5U  H10  H  HCH3   0   0.235  -5.0251  -0.0072  -0.4060
 C5U  H13  H  HNH1   0   0.415   0.2243   3.7295   1.1458
 C5U  H17  H  HCH1   0   0.287   0.0108  -0.2654  -1.2840
 C5U  H18  H  HCR6   0   0.273  -0.3442   0.6066   2.2818
 C5U  H19  H  HCR6   0   0.273   0.1537  -3.3513   3.7962
 C5U  H20  H  HCR6   0   0.289   0.5699  -4.1606   1.5156
 C5U  H21  H  HCH3   0   0.268  -2.9651   2.8382   1.2419
 C5U  H22  H  HCH3   0   0.254  -1.7877   4.1411   1.2767
 C5U  H23  H  HCH3   0   0.272  -2.5933   3.7248  -0.2293
 C5U  N21  N  N      1   0.330   0.5504  -2.8328  -0.6922

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 C5U  C13  O12  single    1.425  0.020  1.425
 C5U  O12  C10  single    1.335  0.020  1.335
 C5U  O11  C10  double    1.213  0.020  1.213
 C5U  C18  C17  aromatic  1.387  0.020  1.387
 C5U  C18  C19  aromatic  1.381  0.020  1.381
 C5U  C17  C16  aromatic  1.384  0.020  1.384
 C5U  C10  C09  single    1.462  0.020  1.462
 C5U  C19  C20  aromatic  1.392  0.020  1.392
 C5U  C16  C15  aromatic  1.396  0.020  1.396
 C5U  C20  C15  aromatic  1.396  0.020  1.396
 C5U  C20  N21  single    1.459  0.020  1.459
 C5U  C24  C08  single    1.498  0.020  1.498
 C5U  C15  C14  single    1.529  0.020  1.529
 C5U  C09  C08  double    1.357  0.020  1.357
 C5U  C09  C14  single    1.521  0.020  1.521
 C5U  N21  O22  single    1.205  0.020  1.205
 C5U  N21  O23  double    1.211  0.020  1.211
 C5U  C08  N07  single    1.366  0.020  1.366
 C5U  C14  C05  single    1.518  0.020  1.518
 C5U  C05  C06  double    1.355  0.020  1.355
 C5U  C05  C02  single    1.464  0.020  1.464
 C5U  N07  C06  single    1.370  0.020  1.370
 C5U  O03  C02  single    1.330  0.020  1.330
 C5U  O03  C04  single    1.425  0.020  1.425
 C5U  C06  C25  single    1.500  0.020  1.500
 C5U  C02  O01  double    1.211  0.020  1.211
 C5U  C13  H1   single    0.970  0.020  1.090
 C5U  C13  H2   single    0.970  0.020  1.090
 C5U  C13  H3   single    0.970  0.020  1.090
 C5U  C17  H4   single    0.930  0.020  1.080
 C5U  C24  H5   single    0.970  0.020  1.090
 C5U  C24  H6   single    0.970  0.020  1.090
 C5U  C24  H7   single    0.970  0.020  1.090
 C5U  C04  H8   single    0.970  0.020  1.090
 C5U  C04  H9   single    0.970  0.020  1.090
 C5U  C04  H10  single    0.970  0.020  1.090
 C5U  N07  H13  single    0.860  0.020  1.020
 C5U  C14  H17  single    0.970  0.020  1.090
 C5U  C16  H18  single    0.930  0.020  1.080
 C5U  C18  H19  single    0.930  0.020  1.080
 C5U  C19  H20  single    0.930  0.020  1.080
 C5U  C25  H21  single    0.970  0.020  1.090
 C5U  C25  H22  single    0.970  0.020  1.090
 C5U  C25  H23  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 C5U  O12  C10  O11  121.62  3.000
 C5U  O11  C10  C09  126.49  3.000
 C5U  O12  C10  C09  111.88  3.000
 C5U  H3   C13  H2   109.16  3.000
 C5U  H3   C13  H1   109.34  3.000
 C5U  H2   C13  H1   109.17  3.000
 C5U  H3   C13  O12  111.55  3.000
 C5U  H2   C13  O12  111.44  3.000
 C5U  H1   C13  O12  106.11  3.000
 C5U  C16  C15  C14  117.28  3.000
 C5U  C14  C15  C20  126.79  3.000
 C5U  C16  C15  C20  115.77  3.000
 C5U  H4   C17  C18  120.32  3.000
 C5U  H4   C17  C16  119.67  3.000
 C5U  C18  C17  C16  120.01  3.000
 C5U  N21  C20  C19  114.60  3.000
 C5U  N21  C20  C15  122.89  3.000
 C5U  C19  C20  C15  122.51  3.000
 C5U  H7   C24  H6   107.43  3.000
 C5U  H7   C24  H5   107.92  3.000
 C5U  H6   C24  H5   108.13  3.000
 C5U  H7   C24  C08  111.20  3.000
 C5U  H6   C24  C08  111.70  3.000
 C5U  H5   C24  C08  110.31  3.000
 C5U  C05  C02  O03  114.97  3.000
 C5U  O03  C02  O01  122.39  3.000
 C5U  C05  C02  O01  122.64  3.000
 C5U  C04  O03  C02  117.39  3.000
 C5U  H10  C04  H9   109.03  3.000
 C5U  H10  C04  H8   109.26  3.000
 C5U  H9   C04  H8   109.28  3.000
 C5U  H10  C04  O03  111.78  3.000
 C5U  H9   C04  O03  111.55  3.000
 C5U  H8   C04  O03  105.86  3.000
 C5U  C14  C05  C06  121.22  3.000
 C5U  C06  C05  C02  124.63  3.000
 C5U  C14  C05  C02  114.03  3.000
 C5U  C25  C06  N07  113.12  3.000
 C5U  C25  C06  C05  128.06  3.000
 C5U  N07  C06  C05  118.82  3.000
 C5U  H13  N07  C08  117.28  3.000
 C5U  H13  N07  C06  117.28  3.000
 C5U  C08  N07  C06  124.72  3.000
 C5U  C09  C08  N07  119.14  3.000
 C5U  N07  C08  C24  113.53  3.000
 C5U  C09  C08  C24  127.32  3.000
 C5U  C14  C09  C08  120.74  3.000
 C5U  C14  C09  C10  119.35  3.000
 C5U  C08  C09  C10  119.90  3.000
 C5U  C13  O12  C10  117.30  3.000
 C5U  H17  C14  C09  108.87  3.000
 C5U  H17  C14  C05  107.41  3.000
 C5U  C09  C14  C05  111.12  3.000
 C5U  H17  C14  C15  109.34  3.000
 C5U  C05  C14  C15  110.70  3.000
 C5U  C09  C14  C15  109.36  3.000
 C5U  H18  C16  C17  118.45  3.000
 C5U  H18  C16  C15  118.90  3.000
 C5U  C17  C16  C15  122.65  3.000
 C5U  H19  C18  C19  119.89  3.000
 C5U  H19  C18  C17  120.96  3.000
 C5U  C19  C18  C17  119.15  3.000
 C5U  H20  C19  C18  119.72  3.000
 C5U  H20  C19  C20  120.37  3.000
 C5U  C18  C19  C20  119.89  3.000
 C5U  H23  C25  H22  107.64  3.000
 C5U  H23  C25  H21  107.81  3.000
 C5U  H22  C25  H21  107.64  3.000
 C5U  H23  C25  C06  111.34  3.000
 C5U  H22  C25  C06  110.41  3.000
 C5U  H21  C25  C06  111.82  3.000
 C5U  O23  N21  O22  123.82  3.000
 C5U  O23  N21  C20  116.86  3.000
 C5U  O22  N21  C20  119.27  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 C5U  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 C5U  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 C5U  CONST_03  C20  C19  C18  C17     0.00   0.0  0
 C5U  CONST_04  C20  C15  C16  C17     0.00   0.0  0
 C5U  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 C5U  CONST_06  C19  C20  C15  C16     0.00   0.0  0
 C5U  CONST_07  C14  C15  C16  C17   180.00   0.0  0
 C5U  CONST_08  C19  C20  C15  C14   180.00   0.0  0
 C5U  CONST_09  N21  C20  C15  C14     0.00   0.0  0
 C5U  CONST_10  N21  C20  C15  C16   180.00   0.0  0
 C5U  CONST_11  N21  C20  C19  C18   180.00   0.0  0
 C5U  CONST_12  H4   C17  C16  C15   180.00   0.0  0
 C5U  CONST_13  H20  C19  C20  C15   180.00   0.0  0
 C5U  CONST_14  H19  C18  C19  C20   180.00   0.0  0
 C5U  CONST_15  H18  C16  C15  C20   180.00   0.0  0
 C5U  Var_01    C08  N07  C06  C05    11.26  30.0  1
 C5U  Var_02    C09  C08  N07  C06   -10.37  30.0  1
 C5U  Var_03    C14  C09  C08  N07    -7.11  30.0  1
 C5U  Var_04    C14  C05  C06  N07     5.43  30.0  1
 C5U  Var_05    O12  C10  C09  C08  -176.49  30.0  1
 C5U  Var_06    H21  C25  C06  C05    50.42  30.0  3
 C5U  Var_07    H5   C24  C08  N07     5.89  30.0  3
 C5U  Var_08    C09  C10  O12  C13   177.12  30.0  3
 C5U  Var_09    C05  C02  O03  C04  -178.39  30.0  3
 C5U  Var_10    H1   C13  O12  C10  -177.02  30.0  3
 C5U  Var_11    H8   C04  O03  C02   178.21  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 C5U  chir_01  C14  C15  C09  C05  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 C5U  plan-1  C15  0.020
 C5U  plan-1  C17  0.020
 C5U  plan-1  C20  0.020
 C5U  plan-1  C14  0.020
 C5U  plan-1  C16  0.020
 C5U  plan-1  C18  0.020
 C5U  plan-1  C19  0.020
 C5U  plan-1  H4   0.020
 C5U  plan-1  H18  0.020
 C5U  plan-1  H19  0.020
 C5U  plan-1  H20  0.020
 C5U  plan-1  N21  0.020
 C5U  plan-2  C20  0.020
 C5U  plan-2  O22  0.020
 C5U  plan-2  O23  0.020
 C5U  plan-2  N21  0.020
 C5U  plan-3  C06  0.020
 C5U  plan-3  N07  0.020
 C5U  plan-3  C08  0.020
 C5U  plan-3  H13  0.020
 C5U  plan-4  C10  0.020
 C5U  plan-4  C09  0.020
 C5U  plan-4  O11  0.020
 C5U  plan-4  O12  0.020
 C5U  plan-5  O01  0.020
 C5U  plan-5  C02  0.020
 C5U  plan-5  O03  0.020
 C5U  plan-5  C05  0.020

